Ok, you're already half way there! Just load winuae, set it so the System.hdf is your main bootable drive, and then set the compact flash as another drive.
Boot up winuae with those settings. Go to hdtoolbox and right click it, then set the tooltype to use uaehf.device instead of scsi.device. When you do that, save it, and then double-click the hdtoolbox icon, and you can use uaehf.device to format and partition your compact flash. Make sure you name id DH0: and set it as bootable. After that, you can format it and use directory opus to copy all of the files from your amiga setup over to the compact flash...then it should work!
